The colonic microbiome is remarkable in that it is amongst the most densely populated microbial habitats on Earth. Several recent high profile reports reveal that the gut microbiome produces substances that are absorbed by the host, which then significantly influence metabolic function. For this reason, the study of gut microbial ecology and its interplay with the host metabolome has emerged as a critical frontier in contemporary nutritional and metabolic research. Recent data from our laboratory and others has unequivocally shown that diet is the principal determinant of the composition of the gut microbiome. Diets low in protein are utilized in the treatment of patients with hepatic encephalopathy, in born errors of metabolism such as urea cycle abnormalities or organic acidemias, and chronic renal failure. Furthermore low protein intake due to disease or insufficient access to food, such as kwashiorkor, can have deleterious effects. Classic studies in physiology have shown that the gut microbiome plays an important role in nitrogen balance of the host. Urea, produced by the host, is hydrolyzed in the colon by urease-producing gut bacteria and the resultant ammonia is absorbed by the host and utilized for protein metabolism. However, no studies have yet scrutinized either the effect of protein restriction on the composition of the gut microbiome or the impact of the microbiome on host nitrogen balance in this setting. In Preliminary Data, we show that there are significant alterations in the composition of the gut microbiome in mice fed a low protein diet and that these mice show evidence of severe metabolic stress, manifested as a striking (40%) increase in calorie consumption simply in order to maintain body weight. In addition, due to a reduction in ureagenesis, these mice suffer a profound defect of water conservation manifested as severe polydypsia and polyuria. The administration of oral antibiotics to these mice dramatically reverses these adverse sequelae. These observations suggest that a low protein diet alters the gut microbiome in a manner that evokes deleterious consequences. We hypothesize that a low protein diet alters the composition and function of the gut microbiome leading to major changes in host metabolism, especially in host nitrogen balance. To address this hypothesis, we will focus on the metabolic interaction between the host and gut microbiome through an analysis of ureagenesis by the host and urea hydrolysis by urease-producing bacteria in the gut. Our proposed project will utilize the expertise of senior investigators with experience in metabolic diseases, deep genomic sequencing, and computational biology assembled for a recently funded NIH pathway initiative grant known as the Human Microbiome Project. We will also take advantage of a unique opportunity to validate our murine findings by characterizing the composition and function of the gut microbiome in human subjects on defined low protein diets as therapy for a rare set of genetic disorders with inborn errors of metabolism such as urea cycle abnormalities and organic acidurias. The results of these studies will, for the first time, determine cause-and-effect relationships between the composition of the gut microbiome (via 16S rDNA phylotyping), bacterial gene representation (via metagenomics), and metabolic function in both mice and humans.

Public Health Relevance

Diets low in protein are utilized in the treatment of patients with hepatic encephalopathy, in born errors of metabolism such as urea cycle abnormalities or organic acidurias, and chronic renal failure. Furthermore low protein intake due to disease or insufficient access to food, such as kwashiorkor, can have deleterious effects. Classic studies in physiology have shown that the gut microbiome plays an important role in nitrogen balance of the host. However, no studies have yet scrutinized either the effect of protein restriction on the composition of the gut microbiome or the impact of the microbiome on host nitrogen balance in this setting. The results of the studies in this proposal will, for the first time, determine cause-and-effect relationships between the composition of the gut microbiome, bacterial gene representation, and host metabolic function in both mice and humans on a low protein diet.